contsurvplot

An R-Package to Visualize the (Causal) Effect of a Continuous Variable on a Time-To-Event Outcome

https://github.com/robindenz1/contsurvplot

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Keywords

causal-inference continuous g-computation survival-analysis visualization

Last synced: 7 months ago · JSON representation

Repository

An R-Package to Visualize the (Causal) Effect of a Continuous Variable on a Time-To-Event Outcome

Basic Info

Host: GitHub
Owner: RobinDenz1
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://robindenz1.github.io/contsurvplot/
Size: 20.4 MB

Statistics

Stars: 14
Watchers: 1
Forks: 1
Open Issues: 2
Releases: 4

Topics

causal-inference continuous g-computation survival-analysis visualization

Created almost 4 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog License Codemeta

contsurvplot

Author: Robin Denz

Description

contsurvplot is an R-Package which can be used to visualize the causal effect of a continuous variable on a time-to-event outcome. It includes multiple different plot types, such as survival area plots, contour plots, heatmaps, survival quantile plots and more. All of them can be adjusted for confounders and all of them have a lot of build in options to customize them according to the users needs. Also, most of the plot functions are based on the ggplot2 package, allowing the user to use the standard ggplot2 syntax to customize the plots further.

Installation

The stable release version can be installed directly from CRAN using:

R install.packages("contsurvplot")

Alternatively, the development version can be installed using the devtools R-Package:

```R library(devtools)

devtools::install_github("RobinDenz1/contsurvplot") ```

or the remotes R-Package:

```R library(remotes)

remotes::install_github("RobinDenz1/contsurvplot") ```

Bug Reports and Feature Requests

If you encounter any bugs or have any specific feature requests, please file an Issue.

Examples

Here are two quick examples using the colon dataset from the survival R-Package. Suppose we want to visualize the effect of the number of lymph nodes with detectable cancer (column nodes) on the survival time. A survival area plot can be produced using the following code:

```R library(contsurvplot) library(ggplot2) library(survival) library(riskRegression)

load colon data

data(cancer)

fit cox model, adjusting for age and sex

model <- coxph(Surv(time, status) ~ age + sex + nodes, data=colon, x=TRUE)

plot survival area

plotsurvarea(time="time", status="status", variable="nodes", data=colon, model=model)

```

Alternatively, we can plot a contour plot to visualize the effect:

R plot_surv_contour(time="time", status="status", variable="nodes", data=colon, model=model)

Or we can use a simple plot of the median survival time as a function of nodes:

R plot_surv_quantiles(time="time", status="status", variable="nodes", data=colon, model=model, p=0.5)

More examples can be found in the documentation and the vignette.

Citation

The main paper associated with this R-Package is:

Robin Denz, Nina Timmesfeld (2023). Visualizing the (causal) effect of a continuous variable on a time-to-event outcome. Epidemiology. 34.5 doi:10.1097/EDE.0000000000001630

In addition, some relevant literature can be found in the documentation pages.

License

The contents of this repository are distributed under the GNU General Public License. You can find the full text of this License in this github repository. Alternatively, see http://www.gnu.org/licenses/.

Owner

Name: Robin Denz
Login: RobinDenz1
Kind: user

Repositories: 2
Profile: https://github.com/RobinDenz1

I am a researcher at the Ruhr-University of Bochum in Germany and am currently enrolled as a PhD Student in "Epidemiology & Clinical Research".

CodeMeta (codemeta.json)

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Total packages: 1
Total downloads:
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Total versions: 4
Total maintainers: 1

cran.r-project.org: contsurvplot

Visualize the Effect of a Continuous Variable on a Time-to-Event Outcome

Homepage: https://github.com/RobinDenz1/contsurvplot
Documentation: http://cran.r-project.org/web/packages/contsurvplot/contsurvplot.pdf
License: GPL (≥ 3)
Latest release: 0.2.2
published 9 months ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 486 Last month

Rankings

Stargazers count: 19.8%

Forks count: 28.8%

Dependent packages count: 29.8%

Average: 31.6%

Dependent repos count: 35.5%

Downloads: 44.3%

Maintainers (1)

robin.denz@rub.de

Last synced: 8 months ago

Dependencies

DESCRIPTION cran

dplyr * imports
foreach * imports
ggplot2 >= 3.0.0 imports
riskRegression * imports
rlang * imports
covr * suggests
doParallel * suggests
gganimate * suggests
knitr * suggests
pammtools * suggests
plotly * suggests
reshape2 * suggests
rmarkdown * suggests
survival * suggests
testthat >= 3.0.0 suggests
transformr * suggests
vdiffr >= 1.0.0 suggests

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